File: __runMe_docker.sh

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trinityrnaseq 2.15.2%2Bdfsg-2
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#!/bin/bash -ve

#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

CPU=$(nproc || sysctl -n hw.physicalcpu)

docker run --rm -v `pwd`:`pwd` trinityrnaseq/trinityrnaseq \
              Trinity --seqType fq --max_memory 2G \
              --left `pwd`/reads.left.fq.gz \
              --right `pwd`/reads.right.fq.gz \
              --SS_lib_type RF \
              --CPU ${CPU} \
              --output `pwd`/trinity_docker_outdir